The 36-year-old unit trust agent had already been charged on Wednesday with 182 counts of sexually abusing the girl.
Yesterday, he claimed trial to charges of sodomising the girl three times daily from Jan 20 to 31, February and between April and July 20 this year, except two days before Ramadan and the first day of the fasting month in May.
He allegedly committed the offence at their apartment in Sungai Way, Petaling Jaya.
The accused's former wife lodged a police report on July 25.
He was charged under Section 377C of the Penal Code for committing carnal intercourse against the order of nature, which carries a maximum of 20 years' jail and whipping upon conviction.
The 36-year-old unit trust agent had already been charged on Wednesday with 182 counts of sexual-related offences.
The man claimed trial to 150 sodomy charges which he allegedly committed between Jan 1 and 19 and the whole month of March; committing incest; abusing the girl and 30 counts of physical sexual assault without intercourse.
In total, he faces 626 charges.
Attorney-General Tan Sri Mohamed Apandi Ali confirmed it was the first such case in the country where a man was facing hundreds of sexual-related offences.
During yesterday's proceedings, the father of three girls appeared calm.
He showed no emotion but hung his head low when the charges were read out to him before Sessions Court judge Yong Zarida Sazali.
He nodded his head, saying he understood the charges.
When asked by the interpreter of the Special Court for Sexual Crimes Against Children whether he claimed trial or pleaded guilty, he said he claimed trial.
None of the accused's family members were present in court.
Deputy public prosecutor Aimi Syazwani Sarmin submitted that the prosecution would not offer bail, as a sodomy offence was non-bailable.
DPP Aimi Syazwani said she was worried the accused would abscond if bail was allowed and that he would harass prosecution witnesses, including the victim.
The man, who was unrepresented, asked for a lower bail.
Judge Yong Zarida denied bail and fixed Sept 18 for mention pending medical and chemist reports.
It is learnt the man divorced two years ago and was given custody of the victim.
His two other younger daughters are staying with their mother.